Best Practices in Method Reporting

Nature Protocols is pleased to be a part of the Resource Identification Initiative, a project aimed at improving the reproducibility of research by clearly identifying key biological resources. Stable unique digital identifiers, called Research Resource Identifiers (RRIDs), are assigned to individual resources, allowing users to accurately identify and source them, track their history, identify known problems (such as cell line contamination and misidentification) and find relevant research papers. Following a successful 6-month trial, we will now require authors to provide RRIDs for all antibodies and cell lines used in their protocols. We will also be encouraging them to add RRIDs for other tools (such as plasmids and organisms) where they think this is helpful.

Effective sharing of experimental methods is crucial to ensuring that others can repeat results. An abundance of tools is available to help.

Documenting experimental methods ensures reproducibility and accountability, and there are innovative ways to disseminate and update them.

Nature Methods is introducing a new article format: Registered Reports. We encourage all authors interested in submitting comparative analyses of the performance of established, related tools or methods to familiarize themselves with this alternative approach to peer review.

Survey sheds light on the ‘crisis’ rocking research.

Here, members of the hCOMET COST Action program provide a consensus statement on the Minimum Information for Reporting Comet Assays (MIRCA).

The CONSORT-AI and SPIRIT-AI extensions improve the transparency of clinical trial design and trial protocol reporting for artificial intelligence interventions.

Reliability of stability data for perovskite solar cells is undermined by a lack of consistency in the test conditions and reporting. This Consensus Statement outlines practices for testing and reporting stability tailoring ISOS protocols for perovskite devices.

This review explores factors to consider when introducing electronic laboratory notebooks, including discussion of integration with research data management and the functionalities to compare when evaluating specific software packages.

Leading voices in the reproducibility landscape call for the adoption of measures to optimize key elements of the scientific process.

Measurements of oxygen consumption rates have been central to the resurgent interest in studying cellular metabolism. To enhance the overall reproducibility and reliability of these measurements, Divakaruni and Jastroch provide a guide advising on the selection of experimental models and instrumentation as well as the analysis and interpretation of data.

Complex microbial communities shape the dynamics of various environments. In this Review, Knight and colleagues discuss the best practices for performing a microbiome study, including experimental design, choice of molecular analysis technology, methods for data analysis and the integration of multiple omics data sets.

Registered Reports were introduced a decade ago as a means for improving the rigour and credibility of confirmatory research. Chambers and Tzavella overview the format’s past, its current status and future developments.

A new standard allows the accuracy of variant calls to be assessed and compared across different technologies, variant types and genomic regions.

Community-developed checklists offer best-practice guidance for biologists preparing light microscopy images and describing image analyses for publications.

A community of researchers working in the emerging field of single-cell proteomics propose best-practice experimental and computational recommendations and reporting guidelines for studies analyzing proteins from single cells by mass spectrometry.

This Perspective, from a large group of metabolomics experts, provides best practices and simplified reporting guidelines for practitioners of liquid chromatography– and gas chromatography–mass spectrometry-based metabolomics.

Comprehensive guidelines and resources to enable accurate reporting for the most common fluorescence light microscopy modalities are reported with the goal of improving microscopy reporting, rigor and reproducibility.

Lack of best practice guidelines currently limits the application of metabolomics in the regulatory sciences. Here, the MEtabolomics standaRds Initiative in Toxicology (MERIT) proposes methods and reporting standards for several important applications of metabolomics in regulatory toxicology.

Studies employing machine-learning (ML) tools in the chemical sciences often report their evaluations in a heterogeneous way. The evaluation guidelines provided in this Perspective should enable more rigorous ML reporting.

Practitioners in the field of single-cell omics are now faced with diverse options for analytical tools to process and integrate data from various molecular modalities. In an Expert Recommendation article, the authors provide guidance on robust single-cell data analysis, including choices of best-performing tools from benchmarking studies.

Lack of information on authors’ contribution to specific aspects of a study hampers reproducibility and replicability. Here, the authors propose a new, easily implemented reporting system to clarify contributor roles in the Methods section of an article.

The metabolomics literature suffers from ambiguity in the nomenclature for individual metabolites, which introduces a disconnect between publications and leads to misinterpretations. This Comment proposes recommendations for metabolite annotations to engage the scientific community and publishers to adopt a more consistent approach to metabolite nomenclature.

Results from clinical trials can be deemed trustworthy only if they are properly conducted and their methods are fully reported. The SPIRIT and CONSORT checklists, which have improved clinical trial design, conduct and reporting, are being updated to reflect recent advances and improve the assessment of healthcare interventions.

The EQIPD framework for rigor in animal experiments aims to unify current recommendations based on evidence behind their rationale and was prospectively tested for feasibility in multicenter animal experiments.

Statistical tools based on machine learning are becoming integrated into chemistry research workflows. We discuss the elements necessary to train reliable, repeatable and reproducible models, and recommend a set of guidelines for machine learning reports.

Rigorous record-keeping and quality control are required to ensure the quality, reproducibility and value of imaging data. The 4DN Initiative and BINA here propose light Microscopy Metadata Specifications that extend the OME Data Model, scale with experimental intent and complexity, and make it possible for scientists to create comprehensive records of imaging experiments.

A knowledgebase developed for increased the transparency of reporting in spheroid research.

To make machine-learning analyses in the life sciences more computationally reproducible, we propose standards based on data, model and code publication, programming best practices and workflow automation. By meeting these standards, the community of researchers applying machine-learning methods in the life sciences can ensure that their analyses are worthy of trust.

In biomedical studies, the environmental conditions used in mammalian cell culture are often underreported, and are seldom monitored or controlled. Best-practice standards are urgently needed.

A protocol for the electrochemical reduction of nitrogen to ammonia enables isotope-sensitive quantification of the ammonia produced and the identification and removal of contaminants.

Responding to widespread concerns about reproducibility, the Organization for Human Brain Mapping created a working group to identify best practices in data analysis, results reporting and data sharing to promote open and reproducible research in neuroimaging. We describe the challenges of open research and the barriers the field faces.

Quality control of cell lines used in biomedical research is essential to ensure reproducibility. Although cell line authentication has been widely recommended for many years, misidentification, including cross-contamination, remains a serious problem. We outline a multi-stakeholder, incremental approach and policy-related recommendations to facilitate change in the culture of cell line authentication.

'Irreproducibility' is symptomatic of a broader challenge in measurement in biomedical research. From the US National Institute of Standards and Technology (NIST) perspective of rigorous metrology, reproducibility is only one aspect of establishing confidence in measurements. Appropriate controls, reference materials, statistics and informatics are required for a robust measurement process. Research is required to establish these tools for biological measurements, which will lead to greater confidence in research results.

Two surveys of over 1,700 publications whose authors use quantitative real-time PCR (qPCR) reveal a lack of transparent and comprehensive reporting of essential technical information. Reporting standards are significantly improved in publications that cite the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines, although such publications are still vastly outnumbered by those that do not.

Optimism about biomedicine is challenged by the increasingly complex ethical, legal and social issues it raises. Reporting of scientific methods is no longer sufficient to address the complex relationship between science and society. To promote 'ethical reproducibility', we call for transparent reporting of research ethics methods used in biomedical research.